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sbTIV - segmentation-based (estimated) Total Intracranial Volume

Contributors: Bruce Fischl (BF), Doug Greve (DG), Andrew Hoopes (AH), Oula Puonti (OP), Nick Schmansky (NS), Koen Van Leemput (KVL)

Total intracranial volume (TIV/ICV) is an important covariate for volumetric analyses of the brain and brain regions, where it can provide a proxy of brain volume. It is commonly used to correct for head size variation (ie. 'normalize' hippocampal volume size). The gold-standard method is manual delineation of T2 scans. Freesurfer provides its eTIV measure, described on this page, but the approach suffers from its indirect approach: alignment to a T1w atlas, and not by direct segmentation of skull.

There are many other estimation methods, a recent example, where a comparison to freesurfer eTIV is made, is:

Our segmentation-based estimate of total intracranial volume, sbTIV, attempts to provide the measure making use of the skull segmentation output by the Samseg processing stream. The freesurfer utilities mri_sbTIV and mri_segstats both provide this measure, where a skull segmentation volume is provided as input.

Usage

mri_sbTIV --i <skullsegvol> [--o <file>]

mri_sbTIV accepts a binary volume where 1 indicates skull and 0 is empty. It determines the TIV by insert brief description of algorithm here and outputs to stdout the estimate in mm3 (and optionally to the text file named by <file>). Note that mri_sbTIV development is based on a skull segmented by Samseg, but in principle could accept any skull segmentation volume. 

mri_segstats --skullseg <skullsegvol> ...

When a skull segmentation is provided to mri_segstats, the same estimation provided by the algorithm underlying mri_sbTIV is used to insert an additional measure of brain volume to its output summary file. From its help file: 

  5. sbTotalIntracranialVolume (sbTIV) - estimate of the intracranial volume
  based on a skull segmentation. See surfer.nmr.mgh.harvard.edu/fswiki/sbTIV

and as found in aseg.stats: 

# Measure sbTotalIntracranialVolume, sbTIV, segmentation-based estimated Total Intracranial Volume, 1667606.252292, mm^3

Validation

The mri_sbTIV measure was validated against these reference sources:

dataset

description

SASHA

22 subjects, manual TIV from T2 scans

ADNI_T2

42 subjects, manual TIV from T2 scans

Buckner40

40 subjects, eTIV from FS v6.0, and SPM12

ADNI60

60 subjects, eTIV from FS v6.0, and SPM12

ADNI_714_1.5T

714 subjects, eTIV from FS v5.3

ADNI_1150_3T

1150 subjects, eTIV from FS v5.3

IXI_79

70 subjects, eTIV from FS v5.3, and SPM12

The test subjects and scripts are located here: /cluster/fsm/users/samseg/<dataset>.

The SASHA and ADNI_T2 datasets support the primary validation efforts, as this data is based on expert manual segmentations. The other datasets compare against the freesurfer eTIV of nearly 2000 subjects, and SPM12 eTIV from 179 subjects.

Project Notes

Tasks

  • NS - confirm Usage format and Validation plan with Contributors
  • AH,KVL,OP - generate skull_seg.mgz output from current T1-based Samseg stream

  • AH - copy SASHA and ADNI_T2 datasets to samsseg/subjects dirs from locations shown in eTIV page

  • AH - run SPM12 eTIV function on Buckner40, ADNI60 and IXI_79

  • AH - create validation scripts, whereby given a set of sbTIV measures for a dataset, plot against the reference dataset (either manual values or eTIV) see Methods section of eTIV for details on SASHA scripts, and the Malone paper for their approach.

  • AH,BF,DG - devise the sbTIV algorithm
  • AH - create mri_sbTIV and update mri_segstats (per Usage statement above)